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Crystal structure of NXG1-deltayniig in complex with xllg, a xyloglucan derived oligosaccharide
Analyse Crystal structure of NXG1-deltayniig in complex with xllg, a xyloglucan derived… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VH9
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellulase
- EC
- 3.2.1.151, 3.2.1.4
- UniProt
- Q07524
- Ligands
- BGC, XYS, GAL, ZN
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellulase (EC 3.2.1.151, 3.2.1.4) | protein | 266 | 15% helix, 41% strand | Q07524 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 8 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · 6 copies · chains B, A
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.74 | 0.77 | 115 | BGC, XYS, GAL |
| 2 | 95 | 0.42 | 0.78 | 14 | empty |
| 3 | 94 | 0.40 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 589 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2VH9 · Crystal structure of NXG1-deltayniig in complex with xllg, a xyloglucan derived… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q07524
- Elsewhere: RCSB PDB 2VH9 · PDBe 2VH9 · UniProt Q07524
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